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It says that with the denominator layout notation, we interpret differentiation of a scalar with respect to a vector as such: $\frac{\mathrm{d}L}{\mathrm{d}w_1}=[\frac{\mathrm{d}L}{\mathrm{d}w_{11}}\frac{\mathrm{d}L}{\mathrm{d}w_{12}} ... \frac{\mathrm{d}L}{\mathrm{d}w_{1n}}]^T$, $L$ a scalar and $w_1$ an $n$ x $1$ vector.

But what if we represent the scalar $L$ differently? e.g $L=w^Tx$, where $w$, $x \in \Bbb{R}^{n \times1}$.
Then we get $\frac{\mathrm{d}L}{\mathrm{d}w}=\frac{\mathrm{d}(w^Tx)}{\mathrm{d}w}=\frac{\mathrm{d}(x^Tw)}{\mathrm{d}w}=x^T$, which is a $1$ by $n$ vector. Doesn't this result disagree with the denominator layout notation? I read somewhere on the wiki that says one should stick to one type of notation, but if certain types of calculations favors one type of notation over the other, wouldn't that be problematic or confusing?

Indeed, the matrix layouts of derivatives tend to be confusing.
The problem as I see it, is that the matrix layout is an arbitrary representation.
And it already more or less fails if we have more than 2 dimensions, since then we can't properly represent it in a rectangular matrix.
When we take the derivative of a vector function with respect to a vector, what we actually have is a set of scalar functions:
$$\pd {\mathbf f}{\mathbf x} = \left(\pd {f_i}{x_j}\right)$$
That is, forget about the matrix layout.
And when we want to multiply it with a vector $\mathbf v$ to find a directional derivative, which is really an application of the chain rule, what we need to do is:
$$\pd {\mathbf f}{\mathbf x} \cdot \mathbf v = \sum_{i=1}^n \pd {f_i}{x_j} v_j \mathbf e_i$$
where $\mathbf e_i$ is the $i$-th unit vector.

Since as humans we like to represent that in something we can write down, and that fits into how we usually do matrix manipulations, the most natural way that fits in our conventions is:
$$\begin{bmatrix}\pd {f_1}{x_1} & ... & \pd {f_1}{x_n} \\ \vdots & & \vdots \\ \pd {f_n}{x_1} & ... & \pd {f_n}{x_n} \end{bmatrix}
\begin{bmatrix}v_1 \\ \vdots \\ v_n\end{bmatrix}$$
This is the Jacobian form, or numerator layout.
The thing to realize, is that whenever we do something like this, we need to ensure that the elements get multiplied and summed with the right elements.
So if we choose to pick the denominator layout instead, to ensure our conventional matrix product works out, we need to write it as:
$$\begin{bmatrix}v_1 & \dots & v_n\end{bmatrix}\begin{bmatrix}\pd {f_1}{x_1} & ... & \pd {f_n}{x_1} \\ \vdots & & \vdots \\ \pd {f_1}{x_n} & ... & \pd {f_n}{x_n} \end{bmatrix}
$$

Or we can choose to forget about conventional matrix layouts and products, and just write:
$$\sum_{i=1}^n \pd {f_i}{x_j} v_j \mathbf e_i$$
or for short:
$$\pd {f_i}{x_j} v_j$$
following Einstein summation convention.